The Cipher Key Lair is a large pyramid-shaped building surrounded by a lake of purple-tinted water. A long concrete path with a large circular concrete platform connects from the entrance of the Lair to the mainland. Inside the Lair, some electronic doors will only open if a crate is moved onto a certain pressure plate. There are also some offices for scientific studies and office management. Gorigan's office is on the top floor.

Due to the player's Snag Machine having been stolen at this point of the game, Zook's Zangoose cannot be snagged during the first battle against him. After the Snag Machine is recovered from Snagem Hideout, Zook is rematched with the same team as before.

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.

B1F

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.

2F

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.

3F

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.

Trainers with a Poké Ball by their names may be challenged for a rematch after defeating certain bosses. In a rematch they may have higher-level Pokémon, and any Shadow Pokémon previously caught will be replaced.